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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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Singh VS, Tripathi P, Pandey P, Singh DN, Dubey BK, Singh C, Singh SP, Pandey R, Tripathi AK. Dicarboxylate Transporters of Azospirillum brasilense Sp7 Play an Important Role in the Colonization of Finger Millet ( Eleusine coracana) Roots. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:828-840. [PMID: 30688544 DOI: 10.1094/mpmi-12-18-0344-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Azospirillum brasilense is a plant growth-promoting bacterium that colonizes the roots of a large number of plants, including C3 and C4 grasses. Malate has been used as a preferred source of carbon for the enrichment and isolation Azospirillum spp., but the genes involved in their transport and utilization are not yet characterized. In this study, we investigated the role of the two types of dicarboxylate transporters (DctP and DctA) of A. brasilense in their ability to colonize and promote growth of the roots of a C4 grass. We found that DctP protein was distinctly upregulated in A. brasilense grown with malate as sole carbon source. Inactivation of dctP in A. brasilense led to a drastic reduction in its ability to grow on dicarboxylates and form cell aggregates. Inactivation of dctA, however, showed a marginal reduction in growth and flocculation. The growth and nitrogen fixation of a dctP and dctA double mutant of A. brasilense were severely compromised. We have shown here that DctPQM and DctA transporters play a major and a minor role in the transport of C4-dicarboxylates in A. brasilense, respectively. Studies on inoculation of the seedlings of a C4 grass, Eleusine corcana, with A. brasilense and its dicarboxylate transport mutants revealed that dicarboxylate transporters are required by A. brasilense for an efficient colonization of plant roots and their growth.
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Affiliation(s)
- Vijay Shankar Singh
- 1 School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Prajna Tripathi
- 1 School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Parul Pandey
- 1 School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Durgesh Narain Singh
- 2 Laboratory of Synthetic Biology, Division of Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Basant Kumar Dubey
- 2 Laboratory of Synthetic Biology, Division of Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow-226015, India
| | - Chhaya Singh
- 1 School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Surendra Pratap Singh
- 3 Department of Botany, Dayanand Anglo-Vedic (PG) College (Affiliated to CSJM University, Kanpur), Civil Lines, Kanpur-208001, India
| | - Rachana Pandey
- 4 Dr D Y Patil Biotechnology and Bioinformatics Institute, Dr D. Y. Patil Vidyapeeth Pune-411033, India
| | - Anil Kumar Tripathi
- 1 School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India
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Maggi F, M. Tang FH, Riley WJ. The Thermodynamic Links between Substrate, Enzyme, and Microbial Dynamics in Michaelis-Menten-Monod Kinetics. INT J CHEM KINET 2018. [DOI: 10.1002/kin.21163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Federico Maggi
- School of Civil Engineering; The University of Sydney; Sydney 2006 NSW Australia
| | - Fiona H. M. Tang
- School of Civil Engineering; The University of Sydney; Sydney 2006 NSW Australia
| | - William J. Riley
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720
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Iyer B, Rajput MS, Jog R, Joshi E, Bharwad K, Rajkumar S. Organic acid mediated repression of sugar utilization in rhizobia. Microbiol Res 2016; 192:211-220. [PMID: 27664739 DOI: 10.1016/j.micres.2016.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 01/17/2023]
Abstract
Rhizobia are a class of symbiotic diazotrophic bacteria which utilize C4 acids in preference to sugars and the sugar utilization is repressed as long as C4 acids are present. This can be manifested as a diauxie when rhizobia are grown in the presence of a sugar and a C4 acid together. Succinate, a C4 acid is known to repress utilization of sugars, sugar alcohols, hydrocarbons, etc by a mechanism termed as Succinate Mediated Catabolite Repression (SMCR). Mechanism of catabolite repression determines the hierarchy of carbon source utilization in bacteria. Though the mechanism of catabolite repression has been well studied in model organisms like E. coli, B. subtilis and Pseudomonas sp., mechanism of SMCR in rhizobia has not been well elucidated. C4 acid uptake is important for effective symbioses while mutation in the sugar transport and utilization genes does not affect symbioses. Deletion of hpr and sma0113 resulted in the partial relief of SMCR of utilization of galactosides like lactose, raffinose and maltose in the presence of succinate. However, no such regulators governing SMCR of glucoside utilization have been identified till date. Though rhizobia can utilize multitude of sugars, high affinity transporters for many sugars are yet to be identified. Identifying high affinity sugar transporters and studying the mechanism of catabolite repression in rhizobia is important to understand the level of regulation of SMCR and the key regulators involved in SMCR.
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Affiliation(s)
- Bhagya Iyer
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | | | - Rahul Jog
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India; Environmental Molecular Biology Laboratory, Division of Biosphere, Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ekta Joshi
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Krishna Bharwad
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Shalini Rajkumar
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India.
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Scharf BE, Hynes MF, Alexandre GM. Chemotaxis signaling systems in model beneficial plant-bacteria associations. PLANT MOLECULAR BIOLOGY 2016; 90:549-59. [PMID: 26797793 DOI: 10.1007/s11103-016-0432-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/04/2016] [Indexed: 05/07/2023]
Abstract
Beneficial plant-microbe associations play critical roles in plant health. Bacterial chemotaxis provides a competitive advantage to motile flagellated bacteria in colonization of plant root surfaces, which is a prerequisite for the establishment of beneficial associations. Chemotaxis signaling enables motile soil bacteria to sense and respond to gradients of chemical compounds released by plant roots. This process allows bacteria to actively swim towards plant roots and is thus critical for competitive root surface colonization. The complete genome sequences of several plant-associated bacterial species indicate the presence of multiple chemotaxis systems and a large number of chemoreceptors. Further, most soil bacteria are motile and capable of chemotaxis, and chemotaxis-encoding genes are enriched in the bacteria found in the rhizosphere compared to the bulk soil. This review compares the architecture and diversity of chemotaxis signaling systems in model beneficial plant-associated bacteria and discusses their relevance to the rhizosphere lifestyle. While it is unclear how controlling chemotaxis via multiple parallel chemotaxis systems provides a competitive advantage to certain bacterial species, the presence of a larger number of chemoreceptors is likely to contribute to the ability of motile bacteria to survive in the soil and to compete for root surface colonization.
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Affiliation(s)
- Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Gladys M Alexandre
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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Patel DK, Murawala P, Archana G, Kumar GN. Repression of mineral phosphate solubilizing phenotype in the presence of weak organic acids in plant growth promoting fluorescent pseudomonads. BIORESOURCE TECHNOLOGY 2011; 102:3055-3061. [PMID: 21050746 DOI: 10.1016/j.biortech.2010.10.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 10/10/2010] [Accepted: 10/12/2010] [Indexed: 05/30/2023]
Abstract
Two phosphate solubilizing bacteria (PSB), M3 and SP1, were obtained from the rhizosphere of mungbean and sweet potato, respectively and identified as strains of Pseudomonas aeruginosa. Their rock phosphate (RP) solubilizing abilities were found to be due to secretion high amount of gluconic acid. In the presence of malate and succinate, individually and as mixture, the P solubilizing ability of both the strains was considerably reduced. This was correlated with a nearly 80% decrease in the activity of the glucose dehydrogenase (GDH) but not gluconate dehydrogenase (GAD) in both the isolates. Thus, GDH enzyme, catalyzing the periplasmic production of gluconic acid, is under reverse catabolite repression control by organic acids in P. aeruginosa M3 and SP1. This is of relevance in rhizospheric conditions and is a new explanation for the lack of field efficacy of such PSB.
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Affiliation(s)
- Divya K Patel
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, India
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Brandt BW, Kelpin FDL, van Leeuwen IMM, Kooijman SALM. Modelling microbial adaptation to changing availability of substrates. WATER RESEARCH 2004; 38:1003-1013. [PMID: 14769420 DOI: 10.1016/j.watres.2003.09.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2002] [Revised: 09/03/2003] [Accepted: 09/19/2003] [Indexed: 05/24/2023]
Abstract
In their natural environment microorganisms encounter changes in substrate availability, involving either nutrient concentrations or nutrient types. They have to adapt to the new conditions in order to survive. We present a model for slow microbial adaptation, involving the synthesis of new enzymes, in response to changes in the availability of substitutable substrates. The model is based on reciprocal (or mutual) inhibition of expression of both the substrate-specific carriers and the associated assimilatory machinery. The inhibition kinetics is derived from the kinetics of synthesizing units. An interesting property of the adaptation model is that the presence of a single limiting resource results in a constant maximum specific substrate consumption rate for fully adapted microorganisms. Because the maximum specific consumption rate is not a function of substrate concentration, for growth on one substrate, the Monod and Pirt models for instance are still valid. Other adaptation models known to us do not fulfil this property. The simplest version of our model describes adaptation during diauxic growth, using only one preference parameter and one initial condition. The applicability of the model is exemplified by fitting it to published data from diauxic growth experiments.
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Affiliation(s)
- Bernd W Brandt
- Department of Theoretical Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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Abstract
Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla, California.
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9
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Inui M, Vertès AA, Yukawa H. Reverse catabolite repression and the regulation of CO2 fixation in Rhodobacter and related bacteria. Res Microbiol 1996; 147:562-6. [PMID: 9084770 DOI: 10.1016/0923-2508(96)84012-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- M Inui
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
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10
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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Chattopadhyay S, Mukherjee A, Ghosh S. Molecular cloning and sequencing of an operon, carRS of Azospirillum brasilense, that codes for a novel two-component regulatory system: demonstration of a positive regulatory role of carR for global control of carbohydrate catabolism. J Bacteriol 1994; 176:7484-90. [PMID: 8002571 PMCID: PMC197204 DOI: 10.1128/jb.176.24.7484-7490.1994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A pleiotropic carbohydrate mutant, CR17, of Azospirillum brasilense RG (wild type) that assimilates C4 dicarboxylates (succinate and malate) but not carbohydrate (fructose, arabinose, galactose, glycerol, and gluconate) as C sources for growth was used to identify the car (carbohydrate regulation) locus by complementation analysis. The 2.8-kb genomic fragment that complemented the Car- defect of CR17 and overlapped the fru operon (S. Chattopadhyay, A. Mukherjee, and S. Ghosh, J. Bacteriol. 175:3240-3243, 1993) has now been completely sequenced. The sequence contains an operon, carRS, coding for two proteins, CARR and CARS, having 236 and 352 amino acid residues, respectively. The 3'-flanking region of the carRS operon showed sequence homology with the 5' terminus of the fruB gene of a related bacterium, Rhodobacter capsulatus. A complementation study with carRS deletion clones showed that only the carR+ gene was required to complement the Car- defect of CR17, signifying that the carbohydrate pleiotropy was due to a lesion within this gene. Although the 2.8-kb DNA containing the carRS operon when introduced by conjugation into CR17 also complemented the Car- defect, the complemented transconjugant was unable to utilize succinate as a C source. The reason for this is not clear. A sequence analysis of the two protein products strongly suggests that the protein pair may constitute a novel two-component regulatory system for global expression of carbohydrate catabolic pathways in A. brasilense.
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Chattopadhyay S, Mukherjee A, Ghosh S. Azospirillum brasilense locus coding for phosphoenolpyruvate:fructose phosphotransferase system and global regulation of carbohydrate metabolism. J Bacteriol 1993; 175:3240-3. [PMID: 8491742 PMCID: PMC204653 DOI: 10.1128/jb.175.10.3240-3243.1993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Mutants of Azospirillum brasilense unable to grow on fructose include ones affected only on fructose (Fru-) and others impaired on many or all carbohydrates through interference with induction of their specific pathways (Car-). Both types of mutants could be complemented by a cosmid in broad-host-range vector pLAFR1 containing a 27.5-kb genomic insert, Car(-)-complementing activity depending on a 2.2-kb fragment, and Fru(-)-complementing activity depending on an overlapping 9.6-kb fragment.
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Mandal NC, Chakrabartty PK. Succinate-mediated catabolite repression of enzymes of glucose metabolism in root-nodule bacteria. Curr Microbiol 1993. [DOI: 10.1007/bf01575912] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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